Two of Australia's most prestigious Catholic schools have cautiously endorsed same-sex marriage in messages to parents, staff and students, directly rebuking recent statements from church leaders.

While stopping short of advocating a "yes" vote, St Ignatius' College in Sydney and Xavier College in Melbourne appealed to Pope Francis' teachings on love, mercy and non-judgment, and urged the school community to dwell on their own consciences.

The two Jesuit schools have educated generations of Australian politicians. St Ignatius', which is independent of the Catholic system, is the alma mater of former prime minister Tony Abbott and Deputy Prime Minister Barnaby Joyce, while Opposition Leader Bill Shorten attended Xavier College.

Father Chris Middleton, rector of Xavier College, called on the church to reflect on the overwhelming support for marriage equality among young people, and cited an Irish archbishop who called for the church to take "a reality check".

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Father Ross Jones of St Ignatius' College wrote a note to staff and parents about the postal survey.Credit:St Ignatius' College / supplied

"In my experience, there is almost total unanimity amongst the young in favour of same-sex marriage, and arguments against it have almost no impact on them," Father Middleton wrote.

"They are driven by a strong emotional commitment to equality, and this is surely something to respect and admire. They are idealistic in the value they ascribe to love, the primary gospel value."

The rector of St Ignatius', Father Ross Jones, outlined the rights already afforded to same-sex couples in Australia, adding many now wish to marry "for the same reasons as their opposite-sex counterparts".

He argued Catholic couples could "in good conscience" engage in sexual relationships for reasons other than procreation under the "order of reason" school of Natural Law, rather than a physicalist view.

Parents at Xavier College in Melbourne were asked to consider whether denial of same-sex marriage was "unjust discrimination".Credit:Wayne Taylor

"Presumably, same sex-couples, who make such a commitment to each other in good conscience, do so by reflecting on experience and on what it is to be human, using their God-given reason," Father Jones wrote.

In his August 24 letter, Father Middleton sought to downplay the role of religion in the upcoming postal survey. While maintaining the church had a right to participate in the debate, he noted: "The vote relates to marriage as a civil right, and is not in essence about the Catholic sacramental understanding of marriage."

Archbishop Denis Hart of Melbourne stoked concerns with this threat that church staff could be fired.Credit:Eddie Jim

Father Middleton also suggested the church exposed itself to charges of hypocrisy following the revelations of the Royal Commission into Institutional Responses to Child Sexual Abuse.

"To be brutally honest, the church speaking out in controversial areas around sexuality risks being mired in vitriolic attacks on its credibility in the aftermath of the royal commission," he wrote.

St Ignatius College Riverview, one of the country's most elite schools, is Tony Abbott's alma mater.Credit:AFR

The Xavier College rector cited a letter by Archbishop Tim Costelloe​ of Perth, an opponent of same-sex marriage, who wrote that there should be no "unjust discrimination" against same-sex couples.

But Father Middleton turned that around and told parents: "For many Catholics engaged in the debate the critical question is whether the denial of the right to civil marriage is an 'unjust discrimination'?"

A screenshot of Xavier College rector Chris Middleton's letter to parents and students, August 24.

"I do not know if Riverview has any LBGTQI teachers or parents in the college and if they have intentions of marriage: I won't be asking with a view to removing them from the school," he wrote.

"Those of same-sex orientation who are part of our community are welcomed and valued as part of the greater mission of the church, and that is to bring God's love to the world and those in need of it."